Block-copolymer orientation in thin films is controlled by the complex balance between interfacial free energies, including the inter-block segregation strength, the surface tensions of the blocks, and the relative substrate interactions. While block-copolymer lamellae orient horizontally when there is any preferential affinity of one block for the substrate, we recently described how nanoparticle-roughened substrates can be used to modify substrate interactions. We demonstrate how such 'neutral' substrates can be combined with control of annealing temperature to generate vertical lamellae orientations throughout a sample, at all thicknesses. We observe an orientational transition from vertical to horizontal lamellae upon heating, as confirmed using a combination of atomic force microscopy (AFM), neutron reflectometry (NR) and rotational small-angle neutron scattering (RSANS). Using molecular dynamics (MD) simulations, we identify substrate-localized distortions to the lamellar morphology as the physical basis of the novel behavior. In particular, under strong segregation conditions, bending of horizontal lamellae induce a large energetic cost. At higher temperatures, the energetic cost of conformal deformations of lamellae over the rough substrate is reduced, returning lamellae to the typical horizontal orientation. Thus, we find that both surface interactions and temperature play a crucial role in dictating block-copolymer lamellae orientation. Our combined experimental and simulation findings suggest that controlling substrate roughness should provide a useful and robust platform for controlling block-copolymer orientation in applications of these materials.